Starting phenix.real_space_refine on Sun Apr 5 03:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.map" model { file = "/net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9omr_70617/04_2026/9omr_70617.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 36 5.16 5 C 4845 2.51 5 N 1245 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7584 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2455 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 299} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7584 At special positions: 0 Unit cell: (88.168, 86.52, 117.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 9 15.00 O 1449 8.00 N 1245 7.00 C 4845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.02 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.02 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG A 503 " - " ASN A 310 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG B 503 " - " ASN B 310 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " " NAG C 503 " - " ASN C 310 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 326.6 milliseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 24.6% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.624A pdb=" N TYR A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.624A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 45 through 63 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.624A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 98' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 70 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 282 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 70 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 282 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 70 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 70 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 282 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 282 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 193 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2358 1.34 - 1.46: 1895 1.46 - 1.58: 3469 1.58 - 1.70: 15 1.70 - 1.81: 42 Bond restraints: 7779 Sorted by residual: bond pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 7774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10406 1.73 - 3.46: 157 3.46 - 5.19: 15 5.19 - 6.92: 6 6.92 - 8.66: 3 Bond angle restraints: 10587 Sorted by residual: angle pdb=" C ILE C 309 " pdb=" N ASN C 310 " pdb=" CA ASN C 310 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.10e+00 angle pdb=" C ILE B 309 " pdb=" N ASN B 310 " pdb=" CA ASN B 310 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.10e+00 angle pdb=" C ILE A 309 " pdb=" N ASN A 310 " pdb=" CA ASN A 310 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.04e+00 angle pdb=" N ILE C 52 " pdb=" CA ILE C 52 " pdb=" C ILE C 52 " ideal model delta sigma weight residual 110.42 112.30 -1.88 9.60e-01 1.09e+00 3.85e+00 angle pdb=" N ILE B 52 " pdb=" CA ILE B 52 " pdb=" C ILE B 52 " ideal model delta sigma weight residual 110.42 112.30 -1.88 9.60e-01 1.09e+00 3.84e+00 ... (remaining 10582 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 4537 24.58 - 49.16: 179 49.16 - 73.73: 30 73.73 - 98.31: 6 98.31 - 122.89: 9 Dihedral angle restraints: 4761 sinusoidal: 2046 harmonic: 2715 Sorted by residual: dihedral pdb=" C2 NAG B 503 " pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " pdb=" C5 NAG B 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.93 -122.89 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.89 -122.85 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C2 NAG C 503 " pdb=" C1 NAG C 503 " pdb=" O5 NAG C 503 " pdb=" C5 NAG C 503 " ideal model delta sinusoidal sigma weight residual -62.96 59.89 -122.85 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 4758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 711 0.034 - 0.068: 324 0.068 - 0.102: 101 0.102 - 0.136: 58 0.136 - 0.170: 12 Chirality restraints: 1206 Sorted by residual: chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 194 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 194 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 194 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1203 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 289 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 290 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 290 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 290 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 289 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO A 290 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 289 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 290 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 290 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 290 " 0.035 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1074 2.76 - 3.29: 6998 3.29 - 3.83: 12578 3.83 - 4.36: 15003 4.36 - 4.90: 26129 Nonbonded interactions: 61782 Sorted by model distance: nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.224 3.040 nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.225 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.225 3.040 nonbonded pdb=" O GLU A 103 " pdb=" OH TYR B 299 " model vdw 2.299 3.040 nonbonded pdb=" O GLU B 103 " pdb=" OH TYR C 299 " model vdw 2.302 3.040 ... (remaining 61777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.690 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7803 Z= 0.209 Angle : 0.566 8.656 10644 Z= 0.292 Chirality : 0.048 0.170 1206 Planarity : 0.005 0.064 1311 Dihedral : 14.207 122.888 2988 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.49 % Allowed : 4.83 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 939 helix: 0.46 (0.39), residues: 201 sheet: 1.22 (0.29), residues: 333 loop : -0.82 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 302 TYR 0.015 0.001 TYR C 222 PHE 0.006 0.001 PHE B 239 TRP 0.012 0.001 TRP B 268 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 7779) covalent geometry : angle 0.55813 (10587) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.24530 ( 30) hydrogen bonds : bond 0.17246 ( 193) hydrogen bonds : angle 5.75385 ( 507) link_NAG-ASN : bond 0.00483 ( 9) link_NAG-ASN : angle 1.60867 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 223 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 HIS cc_start: 0.7795 (t70) cc_final: 0.7112 (m-70) REVERT: A 254 GLU cc_start: 0.7280 (pp20) cc_final: 0.7043 (pp20) REVERT: A 273 ASP cc_start: 0.8301 (m-30) cc_final: 0.8000 (m-30) REVERT: B 103 GLU cc_start: 0.7425 (mp0) cc_final: 0.7183 (mp0) REVERT: B 148 ASP cc_start: 0.8428 (t0) cc_final: 0.8193 (t0) REVERT: B 149 MET cc_start: 0.8469 (mmt) cc_final: 0.8141 (mmm) REVERT: B 191 MET cc_start: 0.7811 (mtm) cc_final: 0.7484 (mpp) REVERT: B 214 ASN cc_start: 0.8644 (p0) cc_final: 0.8378 (p0) REVERT: B 250 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7110 (mm-30) REVERT: B 254 GLU cc_start: 0.7318 (pp20) cc_final: 0.7101 (pp20) REVERT: B 258 LYS cc_start: 0.8243 (tppt) cc_final: 0.8037 (tppt) REVERT: C 60 VAL cc_start: 0.8500 (p) cc_final: 0.8235 (m) REVERT: C 97 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7798 (mt-10) REVERT: C 143 VAL cc_start: 0.8718 (m) cc_final: 0.8418 (p) REVERT: C 148 ASP cc_start: 0.8169 (t0) cc_final: 0.7950 (t0) REVERT: C 204 HIS cc_start: 0.7747 (t70) cc_final: 0.6868 (m-70) REVERT: C 250 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7515 (mm-30) REVERT: C 254 GLU cc_start: 0.7375 (pp20) cc_final: 0.7095 (pp20) outliers start: 12 outliers final: 10 residues processed: 232 average time/residue: 0.5450 time to fit residues: 133.2777 Evaluate side-chains 212 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 152 ASN C 122 GLN C 201 ASN C 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110826 restraints weight = 10579.286| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.03 r_work: 0.3350 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7803 Z= 0.191 Angle : 0.579 7.417 10644 Z= 0.297 Chirality : 0.052 0.225 1206 Planarity : 0.005 0.061 1311 Dihedral : 14.231 112.606 1330 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.59 % Allowed : 11.03 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 939 helix: 0.01 (0.37), residues: 207 sheet: 1.20 (0.28), residues: 333 loop : -0.76 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.018 0.002 TYR C 235 PHE 0.009 0.001 PHE C 239 TRP 0.019 0.002 TRP B 268 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7779) covalent geometry : angle 0.56935 (10587) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.12681 ( 30) hydrogen bonds : bond 0.04386 ( 193) hydrogen bonds : angle 4.95914 ( 507) link_NAG-ASN : bond 0.00497 ( 9) link_NAG-ASN : angle 1.96189 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 HIS cc_start: 0.7759 (t70) cc_final: 0.7074 (m90) REVERT: A 250 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7543 (mm-30) REVERT: A 254 GLU cc_start: 0.7290 (pp20) cc_final: 0.7072 (pp20) REVERT: A 258 LYS cc_start: 0.8270 (tppt) cc_final: 0.8064 (mmtm) REVERT: A 273 ASP cc_start: 0.8204 (m-30) cc_final: 0.7996 (m-30) REVERT: B 103 GLU cc_start: 0.7562 (mp0) cc_final: 0.7151 (mp0) REVERT: B 137 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8459 (mp) REVERT: B 143 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (p) REVERT: B 149 MET cc_start: 0.8431 (mmt) cc_final: 0.8116 (mmt) REVERT: B 191 MET cc_start: 0.7831 (mtm) cc_final: 0.7519 (mtp) REVERT: B 214 ASN cc_start: 0.8718 (p0) cc_final: 0.8457 (p0) REVERT: B 254 GLU cc_start: 0.7347 (pp20) cc_final: 0.7138 (pp20) REVERT: B 286 ARG cc_start: 0.8022 (ptp90) cc_final: 0.7711 (ptp90) REVERT: C 96 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6527 (tm-30) REVERT: C 97 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 191 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7215 (mtm) REVERT: C 204 HIS cc_start: 0.7799 (t70) cc_final: 0.6950 (m90) outliers start: 29 outliers final: 20 residues processed: 224 average time/residue: 0.5219 time to fit residues: 123.8047 Evaluate side-chains 236 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 19 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 152 ASN C 122 GLN C 267 ASN C 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110583 restraints weight = 10706.935| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.04 r_work: 0.3343 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7803 Z= 0.168 Angle : 0.564 8.190 10644 Z= 0.289 Chirality : 0.051 0.281 1206 Planarity : 0.005 0.059 1311 Dihedral : 13.988 113.684 1330 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.72 % Allowed : 12.39 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.28), residues: 939 helix: 0.07 (0.37), residues: 207 sheet: 1.17 (0.29), residues: 333 loop : -0.73 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 302 TYR 0.013 0.001 TYR B 222 PHE 0.008 0.001 PHE B 336 TRP 0.015 0.002 TRP B 268 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7779) covalent geometry : angle 0.55572 (10587) SS BOND : bond 0.00318 ( 15) SS BOND : angle 1.04133 ( 30) hydrogen bonds : bond 0.03871 ( 193) hydrogen bonds : angle 4.87267 ( 507) link_NAG-ASN : bond 0.00656 ( 9) link_NAG-ASN : angle 1.81718 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 254 GLU cc_start: 0.7268 (pp20) cc_final: 0.7035 (pp20) REVERT: A 258 LYS cc_start: 0.8300 (tppt) cc_final: 0.8066 (mmtm) REVERT: A 273 ASP cc_start: 0.8199 (m-30) cc_final: 0.7993 (m-30) REVERT: B 103 GLU cc_start: 0.7593 (mp0) cc_final: 0.7153 (mp0) REVERT: B 137 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 191 MET cc_start: 0.7784 (mtm) cc_final: 0.7478 (mpp) REVERT: B 214 ASN cc_start: 0.8700 (p0) cc_final: 0.8417 (p0) REVERT: B 223 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7786 (mp) REVERT: B 250 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 254 GLU cc_start: 0.7332 (pp20) cc_final: 0.7115 (pp20) REVERT: C 96 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6550 (tm-30) REVERT: C 97 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7772 (mt-10) REVERT: C 148 ASP cc_start: 0.8105 (t0) cc_final: 0.7893 (t0) REVERT: C 286 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7723 (ptp90) outliers start: 30 outliers final: 25 residues processed: 220 average time/residue: 0.5334 time to fit residues: 124.2402 Evaluate side-chains 236 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110287 restraints weight = 10755.528| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.09 r_work: 0.3335 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7803 Z= 0.181 Angle : 0.582 9.165 10644 Z= 0.295 Chirality : 0.051 0.294 1206 Planarity : 0.005 0.057 1311 Dihedral : 13.610 106.952 1330 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.71 % Allowed : 12.64 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 939 helix: 0.03 (0.37), residues: 207 sheet: 1.10 (0.28), residues: 333 loop : -0.75 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 302 TYR 0.014 0.001 TYR B 222 PHE 0.008 0.001 PHE B 336 TRP 0.016 0.001 TRP B 268 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7779) covalent geometry : angle 0.57213 (10587) SS BOND : bond 0.00331 ( 15) SS BOND : angle 1.07087 ( 30) hydrogen bonds : bond 0.03822 ( 193) hydrogen bonds : angle 4.88356 ( 507) link_NAG-ASN : bond 0.00547 ( 9) link_NAG-ASN : angle 1.97988 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 254 GLU cc_start: 0.7297 (pp20) cc_final: 0.7058 (pp20) REVERT: A 258 LYS cc_start: 0.8286 (tppt) cc_final: 0.8070 (mmtm) REVERT: A 273 ASP cc_start: 0.8184 (m-30) cc_final: 0.7978 (m-30) REVERT: B 91 LYS cc_start: 0.8768 (tptm) cc_final: 0.8548 (tptp) REVERT: B 149 MET cc_start: 0.8201 (mmt) cc_final: 0.7883 (mmt) REVERT: B 191 MET cc_start: 0.7789 (mtm) cc_final: 0.7475 (mpp) REVERT: B 214 ASN cc_start: 0.8704 (p0) cc_final: 0.8464 (p0) REVERT: B 223 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (mp) REVERT: B 250 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7325 (mm-30) REVERT: B 254 GLU cc_start: 0.7342 (pp20) cc_final: 0.7106 (pp20) REVERT: C 60 VAL cc_start: 0.8435 (p) cc_final: 0.8230 (m) REVERT: C 96 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6575 (tm-30) REVERT: C 97 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 148 ASP cc_start: 0.8106 (t0) cc_final: 0.7898 (t0) REVERT: C 223 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7626 (mp) REVERT: C 286 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7732 (ptp90) outliers start: 38 outliers final: 28 residues processed: 223 average time/residue: 0.5094 time to fit residues: 120.3804 Evaluate side-chains 237 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 122 GLN C 267 ASN C 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111079 restraints weight = 10766.993| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.06 r_work: 0.3349 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7803 Z= 0.138 Angle : 0.558 9.078 10644 Z= 0.281 Chirality : 0.050 0.299 1206 Planarity : 0.005 0.056 1311 Dihedral : 13.262 104.365 1330 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.09 % Allowed : 13.88 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.28), residues: 939 helix: 0.20 (0.37), residues: 207 sheet: 1.10 (0.29), residues: 333 loop : -0.72 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.015 0.001 TYR C 98 PHE 0.008 0.001 PHE B 336 TRP 0.012 0.001 TRP B 268 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7779) covalent geometry : angle 0.54816 (10587) SS BOND : bond 0.00288 ( 15) SS BOND : angle 0.90838 ( 30) hydrogen bonds : bond 0.03379 ( 193) hydrogen bonds : angle 4.76147 ( 507) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 1.96684 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 254 GLU cc_start: 0.7279 (pp20) cc_final: 0.7042 (pp20) REVERT: A 258 LYS cc_start: 0.8291 (tppt) cc_final: 0.8082 (mmtm) REVERT: A 273 ASP cc_start: 0.8175 (m-30) cc_final: 0.7972 (m-30) REVERT: B 91 LYS cc_start: 0.8753 (tptm) cc_final: 0.8541 (tptp) REVERT: B 103 GLU cc_start: 0.7598 (mp0) cc_final: 0.7201 (mp0) REVERT: B 191 MET cc_start: 0.7749 (mtm) cc_final: 0.7460 (mpp) REVERT: B 214 ASN cc_start: 0.8676 (p0) cc_final: 0.8387 (p0) REVERT: B 223 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 250 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7284 (mm-30) REVERT: B 254 GLU cc_start: 0.7325 (pp20) cc_final: 0.7116 (pp20) REVERT: B 286 ARG cc_start: 0.8005 (ptp90) cc_final: 0.7723 (ptp90) REVERT: C 96 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6583 (tm-30) REVERT: C 97 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 148 ASP cc_start: 0.8066 (t0) cc_final: 0.7849 (t0) REVERT: C 149 MET cc_start: 0.8481 (mmp) cc_final: 0.8067 (mmp) REVERT: C 223 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7607 (mp) REVERT: C 286 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7698 (ptp90) outliers start: 33 outliers final: 27 residues processed: 222 average time/residue: 0.5122 time to fit residues: 120.6071 Evaluate side-chains 240 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 0.0050 chunk 90 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.0070 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112459 restraints weight = 10554.230| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3378 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7803 Z= 0.113 Angle : 0.552 9.615 10644 Z= 0.276 Chirality : 0.049 0.308 1206 Planarity : 0.004 0.054 1311 Dihedral : 12.881 102.337 1330 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.09 % Allowed : 15.12 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.28), residues: 939 helix: 0.38 (0.37), residues: 204 sheet: 1.12 (0.29), residues: 333 loop : -0.71 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 155 TYR 0.014 0.001 TYR C 98 PHE 0.007 0.001 PHE B 336 TRP 0.010 0.001 TRP B 268 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7779) covalent geometry : angle 0.54155 (10587) SS BOND : bond 0.00255 ( 15) SS BOND : angle 0.82990 ( 30) hydrogen bonds : bond 0.03262 ( 193) hydrogen bonds : angle 4.65203 ( 507) link_NAG-ASN : bond 0.00622 ( 9) link_NAG-ASN : angle 2.04047 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 254 GLU cc_start: 0.7250 (pp20) cc_final: 0.7024 (pp20) REVERT: A 273 ASP cc_start: 0.8139 (m-30) cc_final: 0.7925 (m-30) REVERT: A 358 LEU cc_start: 0.0653 (OUTLIER) cc_final: -0.0330 (tm) REVERT: B 103 GLU cc_start: 0.7522 (mp0) cc_final: 0.7135 (mp0) REVERT: B 148 ASP cc_start: 0.8337 (t0) cc_final: 0.8100 (t0) REVERT: B 191 MET cc_start: 0.7724 (mtm) cc_final: 0.7436 (mpp) REVERT: B 214 ASN cc_start: 0.8638 (p0) cc_final: 0.8360 (p0) REVERT: B 223 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7758 (mp) REVERT: B 250 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 286 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7748 (ptp90) REVERT: C 60 VAL cc_start: 0.8416 (p) cc_final: 0.8211 (m) REVERT: C 94 ASP cc_start: 0.7805 (p0) cc_final: 0.7604 (p0) REVERT: C 96 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6613 (tm-30) REVERT: C 97 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C 141 ASP cc_start: 0.8313 (m-30) cc_final: 0.8074 (m-30) REVERT: C 149 MET cc_start: 0.8403 (mmp) cc_final: 0.7987 (mmp) REVERT: C 223 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7642 (mp) REVERT: C 235 TYR cc_start: 0.8682 (m-80) cc_final: 0.8462 (m-80) REVERT: C 286 ARG cc_start: 0.8110 (ptp90) cc_final: 0.7744 (ptp90) REVERT: C 305 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8567 (mtpp) outliers start: 33 outliers final: 22 residues processed: 225 average time/residue: 0.5100 time to fit residues: 121.7801 Evaluate side-chains 232 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 122 GLN C 201 ASN C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110327 restraints weight = 10702.373| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.07 r_work: 0.3334 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 7803 Z= 0.205 Angle : 0.615 9.681 10644 Z= 0.309 Chirality : 0.052 0.286 1206 Planarity : 0.005 0.054 1311 Dihedral : 13.010 100.049 1330 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.83 % Allowed : 15.37 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 939 helix: 0.17 (0.37), residues: 204 sheet: 1.07 (0.28), residues: 333 loop : -0.84 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 315 TYR 0.015 0.002 TYR C 222 PHE 0.009 0.001 PHE A 252 TRP 0.017 0.002 TRP B 268 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7779) covalent geometry : angle 0.60477 (10587) SS BOND : bond 0.00357 ( 15) SS BOND : angle 1.12499 ( 30) hydrogen bonds : bond 0.03877 ( 193) hydrogen bonds : angle 4.89599 ( 507) link_NAG-ASN : bond 0.00526 ( 9) link_NAG-ASN : angle 2.07104 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 250 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 254 GLU cc_start: 0.7297 (pp20) cc_final: 0.7062 (pp20) REVERT: A 273 ASP cc_start: 0.8200 (m-30) cc_final: 0.7989 (m-30) REVERT: B 91 LYS cc_start: 0.8752 (tptm) cc_final: 0.8537 (tptp) REVERT: B 149 MET cc_start: 0.8356 (mmm) cc_final: 0.8112 (mmm) REVERT: B 214 ASN cc_start: 0.8719 (p0) cc_final: 0.8488 (p0) REVERT: B 223 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (mp) REVERT: B 250 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 286 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7762 (ptp90) REVERT: C 96 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6613 (tm-30) REVERT: C 97 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7723 (mt-10) REVERT: C 141 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (m-30) REVERT: C 223 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 238 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7966 (mt) outliers start: 39 outliers final: 28 residues processed: 220 average time/residue: 0.5296 time to fit residues: 123.4176 Evaluate side-chains 235 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.0980 chunk 89 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 267 ASN C 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112422 restraints weight = 10648.147| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.08 r_work: 0.3376 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7803 Z= 0.118 Angle : 0.572 10.131 10644 Z= 0.287 Chirality : 0.050 0.358 1206 Planarity : 0.004 0.054 1311 Dihedral : 12.818 111.262 1330 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.47 % Allowed : 16.60 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 939 helix: 0.36 (0.38), residues: 204 sheet: 1.08 (0.28), residues: 333 loop : -0.75 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.015 0.001 TYR C 98 PHE 0.008 0.001 PHE B 336 TRP 0.010 0.001 TRP A 268 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7779) covalent geometry : angle 0.56071 (10587) SS BOND : bond 0.00269 ( 15) SS BOND : angle 0.86441 ( 30) hydrogen bonds : bond 0.03207 ( 193) hydrogen bonds : angle 4.68001 ( 507) link_NAG-ASN : bond 0.00730 ( 9) link_NAG-ASN : angle 2.19511 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.5794 (tm) cc_final: 0.5548 (tt) REVERT: A 96 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 152 ASN cc_start: 0.8499 (m110) cc_final: 0.8257 (m110) REVERT: A 250 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 254 GLU cc_start: 0.7255 (pp20) cc_final: 0.7035 (pp20) REVERT: A 358 LEU cc_start: 0.0577 (OUTLIER) cc_final: -0.0332 (tm) REVERT: B 103 GLU cc_start: 0.7539 (mp0) cc_final: 0.7156 (mp0) REVERT: B 214 ASN cc_start: 0.8680 (p0) cc_final: 0.8420 (p0) REVERT: B 223 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7761 (mp) REVERT: B 250 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7307 (mm-30) REVERT: B 286 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7764 (ptp90) REVERT: C 96 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6600 (tm-30) REVERT: C 97 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 141 ASP cc_start: 0.8342 (m-30) cc_final: 0.8094 (m-30) REVERT: C 223 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7653 (mp) REVERT: C 235 TYR cc_start: 0.8700 (m-80) cc_final: 0.8414 (m-80) REVERT: C 286 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7723 (ptp90) REVERT: C 305 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8586 (mtpp) outliers start: 28 outliers final: 23 residues processed: 224 average time/residue: 0.5087 time to fit residues: 120.8355 Evaluate side-chains 230 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 37 optimal weight: 0.9980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 122 GLN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112555 restraints weight = 10462.276| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.06 r_work: 0.3372 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7803 Z= 0.137 Angle : 0.596 9.734 10644 Z= 0.296 Chirality : 0.050 0.331 1206 Planarity : 0.004 0.054 1311 Dihedral : 12.466 106.881 1330 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 16.85 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 939 helix: 0.36 (0.37), residues: 204 sheet: 1.08 (0.28), residues: 333 loop : -0.77 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.015 0.001 TYR C 98 PHE 0.007 0.001 PHE B 336 TRP 0.012 0.001 TRP B 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7779) covalent geometry : angle 0.58303 (10587) SS BOND : bond 0.00289 ( 15) SS BOND : angle 0.95044 ( 30) hydrogen bonds : bond 0.03327 ( 193) hydrogen bonds : angle 4.67533 ( 507) link_NAG-ASN : bond 0.00629 ( 9) link_NAG-ASN : angle 2.35688 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.5789 (tm) cc_final: 0.5548 (tt) REVERT: A 96 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 250 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 254 GLU cc_start: 0.7254 (pp20) cc_final: 0.7025 (pp20) REVERT: A 358 LEU cc_start: 0.0782 (OUTLIER) cc_final: -0.0091 (tm) REVERT: B 214 ASN cc_start: 0.8682 (p0) cc_final: 0.8417 (p0) REVERT: B 223 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7768 (mp) REVERT: B 250 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 286 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7797 (ptp90) REVERT: C 96 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6588 (tm-30) REVERT: C 97 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 141 ASP cc_start: 0.8362 (m-30) cc_final: 0.8112 (m-30) REVERT: C 223 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7622 (mp) REVERT: C 286 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7725 (ptp90) REVERT: C 305 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8577 (mtpp) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 0.5337 time to fit residues: 125.0184 Evaluate side-chains 231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 45 optimal weight: 0.0000 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN C 267 ASN C 280 ASN C 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112997 restraints weight = 10523.354| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.06 r_work: 0.3377 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7803 Z= 0.127 Angle : 0.589 9.363 10644 Z= 0.293 Chirality : 0.050 0.311 1206 Planarity : 0.004 0.054 1311 Dihedral : 12.162 105.318 1330 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 17.22 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 939 helix: 0.45 (0.38), residues: 204 sheet: 1.06 (0.28), residues: 333 loop : -0.75 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.015 0.001 TYR C 98 PHE 0.007 0.001 PHE B 336 TRP 0.009 0.001 TRP B 268 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7779) covalent geometry : angle 0.57496 (10587) SS BOND : bond 0.00272 ( 15) SS BOND : angle 0.89274 ( 30) hydrogen bonds : bond 0.03196 ( 193) hydrogen bonds : angle 4.62518 ( 507) link_NAG-ASN : bond 0.00641 ( 9) link_NAG-ASN : angle 2.46674 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.5822 (tm) cc_final: 0.5578 (tt) REVERT: A 96 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6658 (tm-30) REVERT: A 250 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 254 GLU cc_start: 0.7248 (pp20) cc_final: 0.7018 (pp20) REVERT: A 358 LEU cc_start: 0.1198 (OUTLIER) cc_final: 0.0409 (tm) REVERT: B 103 GLU cc_start: 0.7499 (mp0) cc_final: 0.7119 (mp0) REVERT: B 214 ASN cc_start: 0.8683 (p0) cc_final: 0.8413 (p0) REVERT: B 223 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 250 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 286 ARG cc_start: 0.8029 (ptp90) cc_final: 0.7772 (ptp90) REVERT: C 96 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6623 (tm-30) REVERT: C 97 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 223 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7640 (mp) REVERT: C 238 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 286 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7721 (ptp90) REVERT: C 305 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8569 (mtpp) outliers start: 27 outliers final: 21 residues processed: 222 average time/residue: 0.5156 time to fit residues: 121.3420 Evaluate side-chains 231 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 339 ILE Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 24 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 122 GLN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112981 restraints weight = 10546.944| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.06 r_work: 0.3379 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7803 Z= 0.129 Angle : 0.595 9.532 10644 Z= 0.295 Chirality : 0.051 0.423 1206 Planarity : 0.004 0.054 1311 Dihedral : 12.018 103.259 1330 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 16.98 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.27), residues: 939 helix: 0.49 (0.38), residues: 204 sheet: 1.05 (0.28), residues: 333 loop : -0.74 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.015 0.001 TYR C 98 PHE 0.007 0.001 PHE B 336 TRP 0.010 0.001 TRP B 268 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7779) covalent geometry : angle 0.57814 (10587) SS BOND : bond 0.00288 ( 15) SS BOND : angle 0.94811 ( 30) hydrogen bonds : bond 0.03217 ( 193) hydrogen bonds : angle 4.60998 ( 507) link_NAG-ASN : bond 0.00755 ( 9) link_NAG-ASN : angle 2.71537 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.27 seconds wall clock time: 56 minutes 53.68 seconds (3413.68 seconds total)